Project Summary/Abstract. The Illumina Genome Analyzer IIx will add a needed capability to the core sequencing facility of Penn State's Center for Gene Regulation and Center for Comparative Genomics and Bioinformatics. Our current genomics research with the help of next-generation genome sequencers have advanced our understanding of cancer etiology, chromatin organization, microbial evolution and pathogenesis, and genome organization from extinct mammals. Deeper and more cost-efficient DNA sequencing as afforded by Illumina GA IIx will acceler- ate progress on several of these NIH-funded projects, as it produces a >160 fold increase in the number of mappable reads when compared to our current 454/Roche GS FLX. The capacity of Illumina GA IIx will allow us to more quickly sequence the genomes of extinct or en- dangered mammals. Such information will help us understand how genome composition predisposes organ- isms to extinction in a changing environment. Genetic predisposition due to a lack of genetic diversity is the likely cause of an infectious cancer that is threatening the survival of the Tasmanian Devil, the only surviving marsupial top predator. To better understand such genetic variation and its contribution to species conserva- tion, a large number of alleles need to be probed, and a comprehensive approach that studies all genetic varia- tion in the genome is warranted. The GA IIx will allow comprehensive studies to be conducted in animals that have succumbed to the Tasmanian Facial Tumor Disease, as well as resistant animals. Microbial diversity and genome plasticity will be studied in the bacterium Bordetella. This organism var- ies in host range, pathology/virulence and the ability to cause chronic vs. acute infection. We have established a causal relationship between some of these properties and genome sequence. Illumina GA IIx will enhance our capacity to establish additional phenotype-genotype linkages as outlined in our NIH-funded grant, and thus will accelerate our ability to understand the genetic basis of Bordetella pathogenicity. The Illumina GA IIx will accelerate our research on chromatin organization and gene regulation by in- creasing our genome-wide mapping throughput capacity by >160 fold. ChIP-seq is the highest resolution means of mapping protein locations in the genomes of any organism. The ability of Illumina GA IIx to produce >160 million mappable sequence tags in a single run far surpasses other genome sequencers in throughput, cost, and coverage. Our current capacity is 1 million tags per run using 454/Roche. The ability to handle highly multiplexed samples in a single run makes Illumina GA IIx ideal for ChIP-seq of large genomes (mam- mals) and massively parallel sampling of small genomes (yeast). Illumina GA IIx will be used to dramatically expand our capacity to produce genome-wide maps of nucleosomes and hundreds of transcription factors un- der a variety of environmental states from yeast to flies to humans, as outlined in our funded NIH projects.